OMIA:002149-9913 : Haplotype with homozygous deficiency HH6 in Bos taurus
Categories: Mortality / aging (incl. embryonic lethal)
Links to MONDO diseases: No links.
Mendelian trait/disorder: yes
Mode of inheritance: Autosomal recessive lethal
Considered a defect: yes
Key variant known: yes
Year key variant first reported: 2018
Species-specific symbol: HH6
History: Fritz et al. (2018) "adopted the nomenclature HH6 . . . to acknowledge the previous discoveries and molecular characterizations of the HH1 [OMIA 000001-9913], HH3 [OMIA 001824-9913], HH4 [OMIA 001826-9913], and HH5 [OMIA 001941-9913] embryonic lethal mutations. The HH6 haplotype and HH6 mutation studied in this article should not be confused with the haplotype provisionally named HH6 in Fritz et al. (2013), which was actually associated with the mutation causing complex vertebral malformation" [OMIA 001340-9913].
Mapping: Using the homozygous haplotype deficiency strategy, Fritz et al. (2018) mapped an autosomal recessive embryonic lethal trait to a 1.1Mb region on chromosome BTA16.
Molecular basis: Within the mapped candidate region (see Mapping section), Fritz et al. (2018) identified a likely causal variant as "an A-to-G transition at position 29,773,628 bp on chromosome 16 (g.29773628A>G; rs434666183)". The authors explained that "This A-to-G transition changes the initiator ATG (methionine) codon to ACG because the gene is transcribed on the reverse strand. . . . Initiation of translation at the closest in-frame Met codon would truncate SDE2 by 83 amino acids, including an 8-amino acid motif conserved among eukaryotes".
Breed: Holstein (black and white) (Cattle) (VBO_0000237).
|Symbol||Description||Species||Chr||Location||OMIA gene details page||Other Links|
|SDE2||SDE2 telomere maintenance homolog (S. pombe)||Bos taurus||16||NC_037343.1 (29020714..29005211)||SDE2||Homologene, Ensembl , NCBI gene|
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WARNING! Inclusion of a variant in this table does not automatically mean that it should be used for DNA testing. Anyone contemplating the use of any of these variants for DNA testing should examine critically the relevant evidence (especially in breeds other than the breed in which the variant was first described). If it is decided to proceed, the location and orientation of the variant sequence should be checked very carefully.
Since October 2021, OMIA includes a semiautomated lift-over pipeline to facilitate updates of genomic positions to a recent reference genome position. These changes to genomic positions are not always reflected in the ‘acknowledgements’ or ‘verbal description’ fields in this table.
|OMIA Variant ID||Breed(s)||Variant Phenotype||Gene||Allele||Type of Variant||Source of Genetic Variant||Reference Sequence||Chr.||g. or m.||c. or n.||p.||Verbal Description||EVA ID||Inferred EVA rsID||Year Published||PubMed ID(s)||Acknowledgements|
|990||Holstein (black and white) (Cattle)||Abortion due to haplotype HH6||SDE2||start-lost||Naturally occurring variant||ARS-UCD1.2||16||g.29020700A>G||c.2T>C||p.(M1?)||ENSBTAT00000016992.6:c.2T>C ENSBTAP00000016992.5:p.Met1? "This A-to-G transition changes the initiator ATG (methionine) codon to ACG because the gene is transcribed on the reverse strand. . . . Initiation of translation at the closest in-frame Met codon would truncate SDE2 by 83 amino acids, including an 8-amino acid motif conserved among eukaryotes"||rs434666183||rs434666183||2018||29680649|
Cite this entry
Note: the references are listed in reverse chronological order (from the most recent year to the earliest year), and alphabetically by first author within a year.
|2023||Bengtsson, C., Stålhammar, H., Thomasen, J.R., Fikse, W.F., Strandberg, E., Eriksson, S. :|
|Mating allocations in Holstein combining genomic information and linear programming optimization at the herd level. J Dairy Sci :, 2023. Pubmed reference: 37028963 . DOI: 10.3168/jds.2022-22926.|
|2019||Kamiński, S. :|
|Missense mutation in SDE2 gene - new lethal defect transmitted into Polish Holstein-Friesian cattle. Pol J Vet Sci 22:627-630, 2019. Pubmed reference: 31560480 . DOI: 10.24425/pjvs.2019.129974.|
|2018||Fritz, S., Hoze, C., Rebours, E., Barbat, A., Bizard, M., Chamberlain, A., Escouflaire, C., Vander Jagt, C., Boussaha, M., Grohs, C., Allais-Bonnet, A., Philippe, M., Vallée, A., Amigues, Y., Hayes, B.J., Boichard, D., Capitan, A., Fritz, S., Hoze, C., Rebours, E., Barbat, A., Bizard, M., Chamberlain, A., Escouflaire, C., Vander Jagt, C., Boussaha, M., Grohs, C., Allais-Bonnet, A., Philippe, M., Vallée, A., Amigues, Y., Hayes, B.J., Boichard, D., Capitan, A. :|
|An initiator codon mutation in SDE2 causes recessive embryonic lethality in Holstein cattle. J Dairy Sci 101:6220-6231, 2018. Pubmed reference: 29680649 . DOI: 10.3168/jds.2017-14119.|
- Changed by Frank Nicholas on 20 Apr 2018
- Created by Frank Nicholas on 20 Apr 2018
- Changed by Imke Tammen2 on 20 Jan 2023